BioPerl-1.6.924

NAME

SYNOPSIS

Proof of principle. Not for production use.

DESCRIPTION

This adaptor is a proof-of-principle. It is used to fetch BioFetch sequences into a Bio::DB::GFF database (currently uses a hard-coded EMBL database) as needed. This allows the Generic Genome Browser to be used as a Genbank/EMBL browser.

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright 2002 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

new

Title : new
Usage : $db = Bio::DB::GFF->new(-adaptor=>'biofetch',@args)
Function: create a new adaptor
Returns : a Bio::DB::GFF object
Args : -adaptor : required. Which adaptor to use; biofetch for mysql, biofetch_oracle for Oracle
-preferred_tags : optional. A hash of {classname => weight,...}
used to determine the class and name of the feature
when a choice of possible feature classes is available
(e.g. a feature has both a 'gene' and a 'locus' tag).
Common defaults are provided that work well for eukaryotic
features (but not well for viral/prokaryotic)
see below for additional arguments.
Status : Public

This is the constructor for the adaptor. It is called automatically by Bio::DB::GFF->new. In addition to arguments that are common among all adaptors, the following class-specific arguments are recgonized:

-dsn,-user and -pass indicate the local database to cache results in, and as are per Bio::DB::GFF::Adaptor::dbi. The -proxy argument allows you to set the biofetch web proxy, and uses the same syntax described for the proxy() method of Bio::DB::WebDBSeqI, except that the argument must be passed as an array reference.